REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K4me3, rabbit, monoclonal	Millipore	Cat# 04-745; RRID: AB_1163444
H3K9me3, rabbit, polyclonal	Abcam	Cat# ab8898; RRID: AB_306848
H3K27me3, rabbit,	Active Motif	Cat# 39155; RRID: AB_2561020
Anti 5-bromodeoxyuridine, mouse, monoclonal	Exbio	Cat# 11-286-C100; RRID: AB_10732986
Anti-HMGA2	Abcam	Cat# ab97276; RRID: AB_10679322
Chemicals, Peptides, and Recombinant Proteins
siRNA-DNMT1	GE Healthcare Dharmacon	M-004605-01-0010
siRNA-DNMT3A	GE Healthcare Dharmacon	M-006672-03-0005
siRNA-DNMT3B	GE Healthcare Dharmacon	M-006395-01-0005
siRNA-NT4	GE Healthcare Dharmacon	D-0012-10-04-20
siRNA-HMGA1	GE Healthcare Dharmacon	MQ-004597-02-0010
siRNA-HMGA2	GE Healthcare Dharmacon	M-01349-5-02-0010
siRNA-SUV420H1	GE Healthcare Dharmacon	D-013366-01-0002
siRNA-SUV420H1	GE Healthcare Dharmacon	D-013366-02-0002
siRNA-SUV420H2	GE Healthcare Dharmacon	D-018622-23-0002
siRNA-LRWD1	GE Healthcare Dharmacon	D-016934-01-0002
siRNA-LRWD1	GE Healthcare Dharmacon	D-016934-02-0002
siRNA-RIF1	GE Healthcare Dharmacon	MQ-027983-01-0002
siRNA-GAPDH	GE Healthcare Dharmacon	D-001140-01-20
Lipofectamine RNAiMAX	ThermoFisher Scientific	13778075
Cell Line Nucleofector kit R	Lonza Bioscience	VCA-1001
4-Hydroxy-Tamoxifen	Sigma-Aldrich	H7904
Senescence Beta Galactosidae Staining Kit	Cell Signaling Technology	9806
Critical Commercial Assays
FxCycle, Far Red	ThermoFisher	F10348
TruSeq ChIP Sample Preparation Kit	Illumina	IP-202-1012
TruSeq Stranded Total RNA Library Kit	Illumina	RS-122-2301
NEBNext Ultra DNA Library Prep Kit for Illumina	NEB	E7370
TruSeq DNA Methylation Kit	Illumina	EGMK81312
Deposited Data
Raw Hi-C data generated from WI38 and BJ OIS system	This study	GSE130306
Raw Hi-C data generated from RS system, HSF74 and HSF92 cells	This study	GSE130306
Raw Hi-C data generated from DNMT1 and scramble siRNA treated samples	This study	GSE130306
H3K4me3 ChIP-Seq in OISD0, OISD2, OISD6 and OISD10 cells	This study	GSE130306
H3K4me3 ChIP-Seq in RS-Proliferative and RS- Senescent cells	This study	GSE130306
H3K9me3 ChIP-Seq in OISD0, OISD2, OISD6 and OISD10 cells	This study	GSE130306
H3K9me3 ChIP-Seq in RS-Proliferative and RS- Senescent cells	This study	GSE130306
H3K27me3 ChIP-Seq in OISD0, OISD2, OISD6 and OISD10 cells	This study	GSE130306
H3K27me3 ChIP-Seq in RS-Proliferative and RS- Senescent cells	This study	GSE130306
Strand Specific toatal RNASeq from OISD0, OISD2, OISD4, OISD6 and OISD10 cells	This study	GSE130306
Strand Specific toatal RNASeq from RS-Proliferative and RS- Senescent cells	This study	GSE130306
WGBS DNMT1 depleted OIS cells	This study	GSE130306
WGBS NT depleted OIS cells	This study	GSE130306
Replication timing from OISD0 cells	This study	https://www2.replicationdomain.com/
Replication timing from oncogene induced raf cells at 12 hours, 24 hours and 36 hours	This study	https://www2.replicationdomain.com/
Image data from microscopy images		Mendeley Data, https://doi.org/10.17632/sj8yykm6bn.1
Datasets Reanalyzed
WGBS IMR90	UCSD Human reference Epigenome Mapping Project	GEO GSM432687
WGBS H1	UCSD Human reference Epigenome Mapping Project	GEO GSM429321
WGBS K562	ENCODE	GEO GSE86747
Hi-C data HUVEC Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C data IMR90 Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C data MSC Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C data HUVEC Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C data IMR90 Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C data MSC Proliferative Cells	Zirkel et al., Molecular Cell, VOLUME 70, ISSUE 4, P730-744.E6, MAY 17, 2018	GEO GSE98448
Hi-C dataWI38 raf Proliferative Cells	Chandra et al., Cell Reports, VOLUME 10, ISSUE 4, P471-483, FEBRUARY 03, 2015	ENA PRJEB8073
Hi-C dataWI38 raf oncogene senescent Cells	Chandra et al., Cell Reports, VOLUME 10, ISSUE 4, P471-483, FEBRUARY 03, 2015	ENA PRJEB8073
BJ H3K9me3 ChIP-Seq		GSE87039
BJ Repli-Seq data		GSM923444
Experimental Models: Cell Lines
WI-38hTERT/GFP-RAF1-ER	Jeanblanc et al., 2012	N/A
WI38	From Jean Marc Lemaitre Lab	N/A
BJ-hTERT-B-RAF-V600E	Carvalho et al., 2019	N/A
Skin Fibroblats from 74 year old Human	From Jean Marc Lemaitre used in Genes Dev. 2011 Nov 1; 25(21): 2248–2253	N/A
Software and Algorithms
Shaman R package for a-parametric Hi-C normalization	N/A	https://bitbucket.org/tanaylab/shaman
imageJ	N/A	https://imagej.nih.gov/ij
Bowtie2 v2.2.0	N/A	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools v0.1.19	N/A	http://samtools.sourceforge.net/
DeepTools2	N/A	https://deeptools.readthedocs.io/en/latest/
CSAW	N/A	bioconductor
STAR v2.5	N/A	https://github.com/alexdobin/STAR
DESeq2	N/A	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MACS2	N/A	https://github.com/taoliu/MACS/
SICER2	N/A	https://github.com/bioinf/SICER2
methpipe	Andrew D Smith	http://smithlabresearch.org/software/methpipe/
C-world (Hi-C analysis software)	Job Dekker lab	https://github.com/dekkerlab/cworld-dekker
GraphPad Prism	N/A	https://www.graphpad.com/
MuG VRE	N/A	https://www.multiscalegenomics.eu/MuGVRE/
methpipe	N/A	http://smithlabresearch.org/software/methpipe/